SNU Compbio Lab
Bulletin of the Korean Chemical Society
- A benchmark study of machine learning methods for molecular electronic transition: Tree-based ensemble learning versus graph neural network
- Contribution of Counterion Entropy to the Salt-Induced Transition Between B-DNA and Z-DNA
- Conformational Sampling of Flexible Ligand-binding Protein Loops
- Structural Basis of Functional Conversion of a Floral Repressor to an Activator: A Molecular Dynamics Simulation Study
- Efficiency of Rotational Operators for Geometric Manipulation of Chain Molecules
Journal of Chemical Information and Modeling
- GalaxyWater-CNN: Prediction of Water Positions on the Protein Structure by a 3D-Convolutional Neural Network
- GalaxyWater-wKGB: Prediction of Water Positions on Protein Structure Using wKGB Statistical Potential
- Prediction of Molecular Electronic Transitions Using Random Forests
- GalaxySagittarius: Structure- and Similarity-Based Prediction of Protein Targets for Druglike Compounds
- GalaxyGPCRloop: Template-Based and Ab Initio Structure Sampling of the Extracellular Loops of G-Protein-Coupled Receptors
- Evaluation of GalaxyDock Based on the Community Structure–Activity Resource 2013 and 2014 Benchmark Studies
- GalaxyDock: Protein–Ligand Docking with Flexible Protein Side-chains
Journal of Chemical Theory and Computation
- Dynamic Interactions of Fully Glycosylated SARS-CoV-2 Spike Protein with Various Antibodies
- Structure, Dynamics, Receptor Binding, and Antibody Binding of the Fully Glycosylated Full-Length SARS-CoV-2 Spike Protein in a Viral Membrane
- Potential Application of Alchemical Free Energy Simulations to Discriminate GPCR Ligand Efficacy
- Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations
Journal of Computational Chemistry
- GalaxyDock3: Protein–ligand docking that considers the full ligand conformational flexibility
- GalaxyTongDock: Symmetric and asymmetric ab initio protein–protein docking web server with improved energy parameters
- GalaxyDock2: Protein–ligand docking using beta-complex and global optimization
- LigDockCSA: Protein–ligand docking using conformational space annealing
- Rotational superposition and least squares: The SVD and quaternions approaches yield identical results. Reply to the preceding comment by G. Kneller
- Using quaternions to calculate RMSD
- A kinematic view of loop closure
Journal of Computer-Aided Molecular Design
- GalaxyDock BP2 score: a hybrid scoring function for accurate protein–ligand docking
- Absolute binding free energies for octa-acids and guests in SAMPL5
- Absolute binding free energy calculations of CBClip host–guest systems in the SAMPL5 blind challenge
Journal of Physical Chemistry B
- Developing a Fully Glycosylated Full-Length SARS-CoV-2 Spike Protein Model in a Viral Membrane
- Transition between B-DNA and Z-DNA: Free Energy Landscape for the B−Z Junction Propagation
- Strength of Cα−H···O=C Hydrogen Bonds in Transmembrane Proteins
Methods in Molecular Biology
- Modeling Protein Homo-Oligomer Structures with GalaxyHomomer Web Server. In "Protein Structure Prediction"
- Template-Based Prediction of Protein-Peptide Interactions by Using GalaxyPepDock. In "Modeling Peptide-Protein Interactions"
- Binding Site Prediction of Proteins with Organic Compounds or Peptides Using GALAXY Web Servers. In "Computational Design of Ligand Binding Proteins"
Nucleic Acids Research
- GalaxyHeteromer: protein heterodimer structure prediction by template-based and ab initio docking
- GalaxyRefine2: Simultaneous refinement of inaccurate local regions and overall protein structure
- GalaxyHomomer: a web server for protein homo-oligomer structure prediction from a monomer sequence or structure
- Galaxy7TM: Flexible GPCR-ligand docking by structure refinement
- GalaxyPepDock: a protein–peptide docking tool based on interaction similarity and energy optimization
- GalaxySite: ligand-binding-site prediction by using molecular docking
- GalaxyRefine: protein structure refinement driven by side-chain repacking
- GalaxyWEB server for protein structure prediction and refinement
- The FALC-Loop web server for protein loop modeling
Proteins: Structure, Function, and Bioinformatics
- Modeling SARS-CoV-2 proteins in the CASP-commons experiment
- Protein oligomer structure prediction using GALAXY in CASP14
- Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment
- Assessment of protein model structure accuracy estimation in CASP14: Old and new challenges
- Structure prediction of biological assemblies using GALAXY in CAPRI rounds 38-45
- Prediction of protein oligomer structures using GALAXY in CASP13
- Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment
- Assessment of protein model structure accuracy estimation in CASP13: Challenges in the era of deep learning
- Simultaneous refinement of inaccurate local regions and overall structure in the CASP12 protein model refinement experiment
- The challenge of modeling protein assemblies: the CASP12-CAPRI experiment
- Template-based modeling and ab initio refinement of protein oligomer structures using GALAXY in CAPRI round 30
- Effective protein model structure refinement by loop modeling and overall relaxation
- Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment
- Blind prediction of interfacial water positions in CAPRI
- Community-wide evaluation of methods for predicting the effect of mutations on protein–protein interactions
- Alternative zinc-binding sites explain the redox sensitivity of zinc-containing anti-sigma factors
- New molecular interaction of IIANtr and HPr from Burkholderia pseudomallei identified by X-ray crystallography and docking studies
- Refinement of unreliable local regions in template-based protein models
- Refinement of protein termini in template-based modeling using conformational space annealing
- De novo protein structure prediction by dynamic fragment assembly and conformational space annealing
- Protein loop modeling by using fragment assembly and analytical loop closure
- A statistical rescoring scheme for protein–ligand docking: Consideration of entropic effect
others
ACS Catalysis
ACS Omega
Angewandte Chemie International Edition
- Switchable Nanoporous Sheets by the Aqueous Self-Assembly of Aromatic Macrobicycles
- Self-Dissociating Tubules from Helical Stacking of Noncovalent Macrocycles
BMC Bioinformatics
- GalaxyTBM: template-based modeling by building a reliable core and refining unreliable local regions
Biochemistry
Biodesign
- Accurate protein structure prediction: what comes next?
- Prediction of Protein Structure and Interaction by GALAXY Protein Modeling Programs
Bioinformatics
Biophysical Journal
Chemical Science
Chemosphere
Communications Biology
Current Opinion in Structural Biology
EMBO Molecular Medicine
European Journal of Medicinal Chemistry
Human Mutation
Inflammatory Bowel Diseases
International Journal of Quantum Chemistry
Journal of Biological Chemistry
Journal of Chemical Physics
Journal of Molecular Biology
- GalaxyDomDock: An ab initio domain–domain docking web server for multi-domain protein structure prediction
- Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology
Journal of the Korean Physical Society
Molecular Biology
Nature Communications
- Structural basis of neuropeptide Y signaling through Y1 receptor
- Sclerostin inhibits Wnt signaling through tandem interaction with two LRP6 ectodomains
PLoS ONE
Physical Chemistry Chemical Physics
Proceedings of the National Academy of Sciences
Protein Science
- Structure of vaccinia virus A46, an inhibitor of TLR4 signaling pathway, shows the conformation of VIPER motif
- The flexibility in the proline ring couples to the protein backbone
Science
Scientific Reports
- An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12
- GalaxyRefineComplex: Refinement of protein-protein complex model structures driven by interface repacking